JAL-4083 Use jmolViewer.scriptWait instead of jmolViewer.evalStringQuiet whilst highl...

[jalview.git] / src / jalview / ext / jmol / JalviewJmolBinding.java

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index eee48df..a40da35 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -31,6 +31,8 @@ import java.util.Map;
 import java.util.StringTokenizer;
 import java.util.Vector;
 
+import javax.swing.SwingUtilities;
+
 import org.jmol.adapter.smarter.SmarterJmolAdapter;
 import org.jmol.api.JmolAppConsoleInterface;
 import org.jmol.api.JmolSelectionListener;
@@ -41,10 +43,12 @@ import org.jmol.viewer.Viewer;
 
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
+import jalview.api.FeatureSettingsModelI;
 import jalview.api.SequenceRenderer;
-import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.gui.AppJmol;
 import jalview.gui.IProgressIndicator;
 import jalview.gui.StructureViewer.ViewerType;
 import jalview.io.DataSourceType;
@@ -54,6 +58,7 @@ import jalview.structure.StructureCommand;
 import jalview.structure.StructureCommandI;
 import jalview.structure.StructureSelectionManager;
 import jalview.structures.models.AAStructureBindingModel;
+import jalview.ws.dbsources.Pdb;
 import javajs.util.BS;
 
 public abstract class JalviewJmolBinding extends AAStructureBindingModel
@@ -78,6 +83,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
   public Viewer jmolViewer;
 
+  private boolean globalUseScriptWait = false;
+
   public JalviewJmolBinding(StructureSelectionManager ssm,
           PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
           DataSourceType protocol)
@@ -86,8 +93,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     setStructureCommands(new JmolCommands());
     /*
      * viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter(),
-     * "jalviewJmol", ap.av.applet .getDocumentBase(),
-     * ap.av.applet.getCodeBase(), "", this);
+     * "jalviewJmol", ap.av.applet .getDocumentBase(), ap.av.applet.getCodeBase(),
+     * "", this);
      * 
      * jmolpopup = JmolPopup.newJmolPopup(viewer, true, "Jmol", true);
      */
@@ -117,9 +124,22 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
   private String jmolScript(String script)
   {
-    Cache.log.debug(">>Jmol>> " + script);
-    String s = jmolViewer.evalStringQuiet(script); // scriptWait(script); BH
-    Cache.log.debug("<<Jmol<< " + s);
+    return jmolScript(script, false);
+  }
+
+  private String jmolScript(String script, boolean useScriptWait)
+  {
+    Console.debug(">>Jmol>> " + script);
+    String s;
+    if (globalUseScriptWait || useScriptWait)
+    {
+      s = jmolViewer.scriptWait(script);
+    }
+    else
+    {
+      s = jmolViewer.evalStringQuiet(script); // scriptWait(script); BH
+    }
+    Console.debug("<<Jmol<< " + s);
 
     return s;
   }
@@ -204,8 +224,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       for (int i = 0; i < modelCount; ++i)
       {
         /*
-         * defensive check for null as getModelFileName can return null
-         * even when model count ms.mc is > 0
+         * defensive check for null as getModelFileName can return null even when model
+         * count ms.mc is > 0
          */
         filePath = jmolViewer.ms.getModelFileName(i);
         if (filePath != null && !mset.contains(filePath))
@@ -249,6 +269,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   {
     if (atoms != null)
     {
+      boolean useScriptWait = atoms.size() > 1;
+      boolean prevUseScriptWait = setGlobalUseScriptWait(useScriptWait);
       if (resetLastRes.length() > 0)
       {
         jmolScript(resetLastRes.toString());
@@ -257,14 +279,15 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       for (AtomSpec atom : atoms)
       {
         highlightAtom(atom.getAtomIndex(), atom.getPdbResNum(),
-                atom.getChain(), atom.getPdbFile());
+                atom.getChain(), atom.getPdbFile(), useScriptWait);
       }
+      setGlobalUseScriptWait(prevUseScriptWait);
     }
   }
 
   // jmol/ssm only
   public void highlightAtom(int atomIndex, int pdbResNum, String chain,
-          String pdbfile)
+          String pdbfile, boolean useScriptWait)
   {
     String modelId = getModelIdForFile(pdbfile);
     if (modelId.isEmpty())
@@ -290,7 +313,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     resetLastRes.append(selection).append(";wireframe 0;").append(selection)
             .append(" and not hetero; spacefill 0;");
 
-    jmolScript(cmd.toString());
+    jmolScript(cmd.toString(), useScriptWait);
     jmolHistory(true);
   }
 
@@ -398,8 +421,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     }
 
     /*
-     * highlight position on alignment(s); if some text is returned, 
-     * show this as a second line on the structure hover tooltip
+     * highlight position on alignment(s); if some text is returned, show this as a
+     * second line on the structure hover tooltip
      */
     String label = getSsm().mouseOverStructure(pdbResNum, chainId,
             pdbfilename);
@@ -435,8 +458,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
   /*
    * { if (history != null && strStatus != null &&
-   * !strStatus.equals("Script completed")) { history.append("\n" + strStatus);
-   * } }
+   * !strStatus.equals("Script completed")) { history.append("\n" + strStatus); }
+   * }
    */
 
   public void notifyAtomPicked(int atomIndex, String strInfo,
@@ -497,6 +520,28 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   @Override
   public void notifyCallback(CBK type, Object[] data)
   {
+    /*
+     * ensure processed in AWT thread to avoid risk of deadlocks
+     */
+    SwingUtilities.invokeLater(new Runnable()
+    {
+
+      @Override
+      public void run()
+      {
+        processCallback(type, data);
+      }
+    });
+  }
+
+  /**
+   * Processes one callback notification from Jmol
+   * 
+   * @param type
+   * @param data
+   */
+  protected void processCallback(CBK type, Object[] data)
+  {
     try
     {
       switch (type)
@@ -745,7 +790,9 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       FeatureRenderer fr = getFeatureRenderer(null);
       if (fr != null)
       {
-        fr.featuresAdded();
+        FeatureSettingsModelI colours = new Pdb().getFeatureColourScheme();
+        ((AppJmol) getViewer()).getAlignmentPanel().av
+                .applyFeaturesStyle(colours);
       }
       refreshGUI();
       loadNotifiesHandled++;
@@ -774,8 +821,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   public abstract void sendConsoleEcho(String strEcho); /*
                                                          * { showConsole(true);
                                                          * 
-                                                         * history.append("\n" +
-                                                         * strEcho); }
+                                                         * history.append("\n" + strEcho); }
                                                          */
 
   // /End JmolStatusListener
@@ -1024,4 +1070,11 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   {
     return "http://wiki.jmol.org"; // BH 2018
   }
+
+  private boolean setGlobalUseScriptWait(boolean b)
+  {
+    boolean prev = globalUseScriptWait;
+    globalUseScriptWait = b;
+    return prev;
+  }
 }